How something came into existence shouldn't determine if its intelligence deserves protecting. Creating intelligent machines and torturing them, for instance, should definitely be a criminal act.
And if brain scanning/emulation catches up enough, then what? It's OK to torture a non-human intelligence if the source wasn't a brain scan? What if we start building our own out of composites or scratch?
Intelligence/capacity for suffering should be the deciding factor here. (And hopefully they'll breed more stupid animals for meat, until it's feasible to grow meat directly.)
And that is the whole debate here. Are we willing to let humanity end so AI can give birth to a better AI? I think not.
And don't humans make babies out of non sentient stuff sperm and egg?
Why is it relevant whether they were created from sand and metal by bald apes, or from carbon and water by the autonomous processes that happen in a bald ape's crotch?
It's not. The point is, we build them to serve us, otherwise they are not needed. I don't care if they're sentient or not, their purpose is to serve humanity.
EDIT: you were thinking about Animatrix, weren't you :)
If you give them sentience, they should.